Add docs for sorting track scheme and some UI improvements

README.md

@@ -188,12 +188,35 @@ place.
 
 ### Sort track scheme
 
-#### Sort lineage tree (left-right-anchors)
+#### Sort lineage tree (left-right-landmarks)
+
+* Menu Location: `Plugins > Trees management > Sort trackscheme > Sort lineage tree (left-right-anchors)`
+* Sorts the order of sub lineages in the track scheme.
+* Cell closer to the left landmark, are put to the left side.
+* Cells closer to the right landmark are put to the right side.
+* The user can specify the left and right landmark by selecting tracks.
+* The user can specify if the entire tree should be sorted, only selected subtrees or subtrees with a specific tag.
+* Example: ![sort_lineage_tree_left_right_landmarks.gif](doc/treesmanagement/sort_lineage_tree_left_right_landmarks.gif)
 
 #### Sort lineage tree (extern-intern)
 
+* Menu Location: `Plugins > Trees management > Sort trackscheme > Sort lineage tree (extern-intern)`
+* Sorts the order of the sub lineages in the track scheme.
+* Cells further away from the center landmark, are put to the left side.
+* Cells closer to the center landmark, are put to the right side.
+* The user can specify the center landmark by selecting a track.
+* The user can specify if the entire tree should be sorted, only selected subtrees or subtrees with a specific tag.
+* Example: ![sort_lineage_tree_extern_intern.gif](doc/treesmanagement/sort_lineage_tree_extern_intern.gif)
+
 #### Sort lineage tree (cell life cycle duration)
 
+* Menu Location: `Plugins > Trees management > Sort trackscheme > Sort lineage tree (cell life cycle duration)`
+* Sort selected spots such that the child cell with the longer cell cycle duration (aka branch duration) is arranged to
+  the left in the TrackScheme.
+* If no spots are selected, the entire track scheme is sorted.
+*
+Example: ![sort_lineage_tree_cell_life_cycle_duration.gif](doc/treesmanagement/sort_lineage_tree_cell_life_cycle_duration.gif)
+
 ## Auxiliary displays
 
 ### Show compact lineage

src/main/java/org/mastodon/mamut/tomancak/TomancakPlugins.java

@@ -141,7 +141,7 @@ public class TomancakPlugins extends AbstractContextual implements MamutPlugin
 		menuTexts.put( SET_RADIUS_SELECTED_SPOTS, "Set radius of selected spots" );
 		menuTexts.put( CHANGE_BRANCH_LABELS, "Change branch labels" );
 		menuTexts.put( COMPACT_LINEAGE_VIEW, "Show compact lineage" );
-		menuTexts.put( SORT_TREE, "Sort lineage tree (left-right-anchors)" );
+		menuTexts.put( SORT_TREE, "Sort lineage tree (left-right-landmarks)" );
 		menuTexts.put( SORT_TREE_EXTERN_INTERN, "Sort lineage tree (extern-intern)" );
 		menuTexts.put( SORT_TREE_LIFETIME, "Sort lineage tree (cell life cycle duration)" );
 		menuTexts.put( LABEL_SPOTS_SYSTEMATICALLY, "Systematically label spots (extern-intern)" );
@@ -180,7 +180,7 @@ public void getCommandDescriptions( final CommandDescriptions descriptions )
 			descriptions.add( SET_RADIUS_SELECTED_SPOTS, SET_RADIUS_SELECTED_SPOTS_KEYS, "Set radius for all selected spots." );
 			descriptions.add( CHANGE_BRANCH_LABELS, CHANGE_BRANCH_LABELS_KEYS, "Change the labels of all the spots between to division." );
 			descriptions.add( COMPACT_LINEAGE_VIEW, COMPACT_LINEAGE_VIEW_KEYS, "Show compact representation of the lineage tree.");
-			descriptions.add( SORT_TREE, SORT_TREE_KEYS, "Sort selected spots according to tagged anchors.");
+			descriptions.add( SORT_TREE, SORT_TREE_KEYS, "Sort selected spots according to selectable landmarks." );
 			descriptions.add( SORT_TREE_EXTERN_INTERN, SORT_TREE_EXTERN_INTERN_KEYS, "Sort selected spots according to tagged center anchor.");
 			descriptions.add( SORT_TREE_LIFETIME, SORT_TREE_LIFETIME_KEYS, "Sort selected spots, such that the child cell with the longer cell cycle duration is left in the TrackScheme.");
 			descriptions.add( LABEL_SPOTS_SYSTEMATICALLY, LABEL_SPOTS_SYSTEMATICALLY_KEYS, "Child cells are named after their parent cell, with a \"1\" or \"2\" appended to the label.");

src/main/java/org/mastodon/mamut/tomancak/label_systematically/LabelSpotsSystematicallyDialog.java

@@ -32,6 +32,8 @@
 import javax.swing.JCheckBox;
 import javax.swing.JDialog;
 import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+
 import net.miginfocom.swing.MigLayout;
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.model.Model;
@@ -123,7 +125,8 @@ private void renameButtonClicked()
 			Collection<Spot> center = centerLandmark.getSelectedSpots();
 			if ( center.isEmpty() )
 			{
-				dispose();
+				JOptionPane.showMessageDialog( this, "Please select a center landmark.", "Error",
+						JOptionPane.ERROR_MESSAGE );
 				return;
 			}
 			Collection<Spot> selected = selectSpots.getSelectedSpots();

src/main/java/org/mastodon/mamut/tomancak/sort_tree/SortTreeExternInternDialog.java

@@ -31,6 +31,8 @@
 import javax.swing.JButton;
 import javax.swing.JDialog;
 import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+
 import net.miginfocom.swing.MigLayout;
 import org.mastodon.mamut.ProjectModel;
 import org.mastodon.mamut.model.Spot;
@@ -91,6 +93,11 @@ public static void showDialog(ProjectModel model)
 	private void sortButtonClicked()
 	{
 		Collection<Spot> center = centerLandmark.getSelectedSpots();
+		if ( center.isEmpty() )
+		{
+			JOptionPane.showMessageDialog( this, "Please select a center landmark.", "No center landmark selected",
+					JOptionPane.ERROR_MESSAGE );
+		}
 		Collection<Spot> selectedSpots = nodesToSort.getSelectedSpots();
 		SortTree.sortExternIntern( appModel.getModel(), selectedSpots, center );
 		appModel.getBranchGraphSync().sync();

src/main/java/org/mastodon/mamut/tomancak/sort_tree/SortTreeLeftRightDialog.java

@@ -91,6 +91,24 @@ private void sortButtonClicked()
 		Collection<Spot> left = leftLandmark.getSelectedSpots();
 		Collection<Spot> right = rightLandmark.getSelectedSpots();
 		Collection<Spot> selectedSpot = nodesToSort.getSelectedSpots();
+		if ( left.isEmpty() && right.isEmpty() )
+		{
+			JOptionPane.showMessageDialog( this, "Please select left and right landmarks.", "No landmarks selected",
+					JOptionPane.ERROR_MESSAGE );
+			return;
+		}
+		if ( left.isEmpty() )
+		{
+			JOptionPane.showMessageDialog( this, "Please select left a landmark.", "No left landmark selected",
+					JOptionPane.ERROR_MESSAGE );
+			return;
+		}
+		if ( right.isEmpty() )
+		{
+			JOptionPane.showMessageDialog( this, "Please select right a landmark.", "No right landmark selected",
+					JOptionPane.ERROR_MESSAGE );
+			return;
+		}
 		SortTree.sortLeftRightAnchors( appModel.getModel(), selectedSpot, left, right );
 		appModel.getBranchGraphSync().sync();
 	}